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- EMDB-57471: Cryo-EM structure of mouse heavy-chain apoferritin on continuous ... -

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Basic information

Entry
Database: EMDB / ID: EMD-57471
TitleCryo-EM structure of mouse heavy-chain apoferritin on continuous carbon from 200 kV Glacios
Map datamasked map from relion_postprocess with deposited half maps and mask
Sample
  • Complex: Mouse heavy-chain apoferritin
    • Protein or peptide: Ferritin heavy chain
Keywordsiron storage / cryo-EM benchmark / METAL BINDING PROTEIN
Function / homology
Function and homology information


Iron uptake and transport / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / negative regulation of ferroptosis / ferroxidase activity / negative regulation of fibroblast proliferation / endocytic vesicle lumen / Neutrophil degranulation / ferric iron binding ...Iron uptake and transport / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / negative regulation of ferroptosis / ferroxidase activity / negative regulation of fibroblast proliferation / endocytic vesicle lumen / Neutrophil degranulation / ferric iron binding / autophagosome / iron ion transport / ferrous iron binding / intracellular iron ion homeostasis / immune response / iron ion binding / negative regulation of cell population proliferation / mitochondrion / extracellular region / membrane / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
Ferritin heavy chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.62 Å
AuthorsFromm SA / Mattei S
Funding support Germany, 1 items
OrganizationGrant numberCountry
Boehringer Ingelheim Fonds (BIF) Germany
CitationJournal: To Be Published
Title: LowDoseWizard - rapid and standardised setup of low dose cryo-TEM imaging in SerialEM
Authors: Fromm SA / Mattei S
History
DepositionApr 16, 2026-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_57471.png

Downloads & links

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Map

FileDownload / File: emd_57471.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmasked map from relion_postprocess with deposited half maps and mask
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.69 Å/pix.
x 384 pix.
= 263.424 Å		0.69 Å/pix.
x 384 pix.
= 263.424 Å		0.69 Å/pix.
x 384 pix.
= 263.424 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.686 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.28726134 - 0.70191634
Average (Standard dev.)0.00065518194 (±0.019742206)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 263.424 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_57471_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_57471_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_57471_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mouse heavy-chain apoferritin

EntireName: Mouse heavy-chain apoferritin
Components
  • Complex: Mouse heavy-chain apoferritin
    • Protein or peptide: Ferritin heavy chain

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Supramolecule #1: Mouse heavy-chain apoferritin

SupramoleculeName: Mouse heavy-chain apoferritin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 500 KDa

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Macromolecule #1: Ferritin heavy chain

MacromoleculeName: Ferritin heavy chain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTTASPSQVR QNYHQDAEAA INRQINLELY ASYVYLSMSC YFDRDDVALK NFAKYFLHQS HEEREHAEK LMKLQNQRGG RIFLQDIKKP DRDDWESGLN AMECALHLEK SVNQSLLELH K LATDKNDP HLCDFIETYY LSEQVKSIKE LGDHVTNLRK MGAPEAGMAE YLFDKHTLGH GD ES

UniProtKB: Ferritin heavy chain

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMHEPES
80.0 mMsodim chlorideNaCl
1.7 mMDTT
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR / Details: Quorum GloQube, 25 mA, negative polarity
VitrificationCryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 281 K / Instrument: LEICA EM GP / Details: front side blotting.

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 3033 / Average exposure time: 2.0 sec. / Average electron dose: 40.0 e/Å2 / Details: saved as EER
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 20.0 µm / Calibrated magnification: 204230 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 750421
CTF correctionSoftware - Name: cryoSPARC (ver. 5.0.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-initio
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 1.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 5.0.0) / Number images used: 693767
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 5.0.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 5.0.0)
FSC plot (resolution estimation)

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